Abstract: Coated fuel particles dispersed in graphite matrix were used in high-temperature gas-cooled reactor (HTR). Thousands of coated particles in a fuel pebble and thousands of pebbles in the core arouse the double heterogeneity effects in pebble bed HTR. Actually the distribution of particles and pebbles is random. The random distribution may affect some reactor parameters. Some models with random distribution of the particles were setup, evaluated by MCNP, and compared with regular distribution model, as a result, the effect of random distribution on effective multiplying factor were analyzed. The results show that effective multiplying factor of the random distribution model is a little larger than that of the regular distribution model, and the deviation between the two models is caused by the distribution of fuel particles in space and angle.